There are several ways to measure the thickness of a thin polymer layer but the simplest is ellipsometry. In that case you need to feed in exact refractive index of the layer in ellipsometry program. If you have two layers the one above the other , choose the first one from down to the surface layer. And you should estimate the thickness of each layer. Then when you measure, you will have the final thickness of the layers together.
You can also use attenuated total reflection (ATR)-Fourier transform infrared (FT-IR) spectroscopy or infrared frustrated total internal reflection (FTIR) spectroscopy. These methods are based on an analytic expression derived for the dependence of the intensities of absorption bands in IR FTIR spectra on the thickness of a polymer layer.
A rough estimate can be made by integrating the charge (e.g. the area under the CV curve) and estimating the mass using the Faraday's law and known stoichiometry.